BCHM 4611 Final Exam 2025

BCHM 4611 Final Exam 2025 Prokaryotes - -2 domains: archaea and bacteria, exclusively single cell organisms, no nucleus Benefits of being prokaryotic - -More adaptable to changing environments, species have evolved to colonize extreme environments due to their simplicity and rapid cell division Eukaryotes - -Multicellular and unicellular organisms, more complex cellular organization with membrane-enclosed organelles that have specialized functions, DNA stored in nucleus Classes of monomers - -Amino acids, monosaccharides, nucleotides, and lipids Classes of polymers - -Polypeptides, polysaccharides, nucleic acids (no true polymers for lipids - form non-covalent aggregates) Polypeptide/protein - -Polymer of amino acids linked together by peptide bonds Residue - -Monomer that has been incorporated into a polymer Protein major roles - -Carry out metabolic reactions, support cellular structures Protein minor role - -Store energy Nucleic acid major role - -Encode information Nucleic acid minor roles - -Carry out metabolic reactions, support cellular structures Polysaccharides major roles - -Store energy, support cellular structures Polysaccharides minor role - -Encode information Open system - -Energy can be transferred between the system and its surroundings Closed system - -Only exchanges energy with its surroundings, not matter Isolated system - -Does not exchange energy or matter with its surroundings Gibbs free energy (G) - -Thermodynamic quantity whose change indicates the spontaneity of a process. For spontaneous/favorable processes, ΔG 0, whereas for a process at equilibrium, ΔG = 0 BCHM 4611 BCHM 4611 Enthalpy (H) - -Heat content of a biochemical system Entropy (S) - -Degree of randomness or disorder of a system Free energy change equation - -ΔG = ΔH - TΔS Coupled reaction - -Reactions that occur in concert with each other; product of the first reaction is a reactant for the second reaction; ΔG values are added when reactions are combined Why is ΔG independent of path chosen? - -Depends only on the initial and final states of the system, without regard to the specific chemical or mechanical work that occurred in going from one state to the other Oxidation - -Loss of electrons through the addition of oxygen or removal of hydrogen; oxidation of carbon is thermodynamically favorable so it can be coupled with otherwise unfavorable processes Catabolism - -Breaking down molecules, yielding energy; some of this free energy may be conserved in the formation of nucleotide triphosphates (NTPs) such as ATP or reduced cofactors such as NADP+ or Q Anabolism - -Building complex molecules at the expense of energy H2O structure/geometry - -Central oxygen atom forms covalent bonds with two hydrogen atoms, leaving two unshared pairs of electrons; tetrahedral geometry How does water's structure affect its properties and interactions with other molecules? - -It is polar (uneven distribution of charge) which allows it to form hydrogen bonds with other water molecules, this makes water highly cohesive; has high dielectric constant which means ionic compounds dissolve in it well; polar compounds also dissolve well due to hydrogen bonding with water Covalent bond - -Formed when two atoms share electrons Ionic interaction - -Electrostatic interaction between two groups that is stronger than a hydrogen bond but weaker than a covalent bond Hydrogen bond - -Partly electrostatic, partly covalent interaction between a donor group such as OH or NH and an electronegative acceptor atom such as O or N Types of Van der Waals interactions - -Dipole-dipole, dipole-induced dipole, and London dispersion forces BCHM 4611 BCHM 4611 Van der Waals interactions - -Weak non-covalent association between molecules that arises from the attractive forces between polar groups (dipole-dipole interactions) or between non-polar groups whose fluctuating electron distribution gives rise to temporary dipoles (London dispersion forces) Relative strengths of chemical bonds (weakest to strongest) - -Van der Waals, hydrogen bond, ionic, covalent Amphipathic/amphiphilic - -Having both polar and non-polar regions and therefore being both hydrophilic and hydrophobic How do amphiphilic molecules behave in aqueous solutions? - -Polar groups of amphiphiles orient themselves toward the solvent molecules and are therefore hydrated, while the nonpolar groups tend to aggregate due to the hydrophobic effect; as a result, amphiphiles may form a spherical micelle, a particle with a solvated surface and a hydrophobic core Hydrophobic effect - -Exclusion of non-polar substances from an aqueous solution; non polar molecules are driven out of the aqueous phase by the unfavorable entropy cost of individually hydrating them Buffer - -Solution containing an acid and its conjugate base, resists changes in pH when more acid or base is added Buffer effective range - -Within one unit of the pKa (pKa +/- 1) Bicarbonate buffer system - -CO2 in blood plasma reacts with water to form carbonic acid, H2CO3, which ionizes to HCO3- Why is bicarbonate buffer system effective? - -Excess hydrogen ions can not only be buffered but can also be eliminated from the body because after the H+ combines with HCO3− to re-form H2CO3 (which rapidly equilibrates with CO2 + H2O), some of the CO2 can be given off as a gas in the lungs; breathing can be adjusted to help control blood pH What determines whether a reaction is spontaneous or not? - -The sign of the change in free energy (ΔG) of the reaction What determines the rate of the reaction? - -The magnitude of the activation energy (ΔG‡) The reaction coordinate for covalent catalysis has... - -Two peaks, with a trough in between them where the stable intermediate is formed BCHM 4611 BCHM 4611 In the chymotrypsin reaction, how is the tetrahedral intermediate stabilized? - -Oxyanion hole stabilization through hydrogen bonding with H's on Ser195 and Gly193 Competitive inhibitor - -Competes with the substrate for binding at the enzyme's active site; frequently resemble the substrate or product of a reaction The best competitive inhibitors... - -Mimic the transition state of the reaction Triacylglycerols (triglycerides) - -A glycerol molecule esterified to three fatty acid molecules; the most common form of fatty acid storage Integral membrane proteins - -Have hydrophobic peptide regions embedded in the lipid bilayer and these proteins require strong detergents to isolate Peripheral membrane proteins - -Associate with the polar head groups of membrane lipids or with the exposed regions of other membrane proteins; can be isolated with mild salt solutions which will compete to bind with these regions Lipid-linked proteins - -Insert a hydrophobic anchor into the membrane Types of lipid-linked proteins - -Myristoylated, palmitoylated, prenylated, and GPI-linked Myristoylated protein - -A myristoyl group (C14:0) attached to an N-term Gly via an amide linkage Palmitoylated protein - -A palmitoyl group (C16:0) reversibly attached to a Cys side chain via a thioester linkage Prenylated protein - -An isoprenoid group linked to a C-term Cys via a thiother linkage GPI-linked proteins - -GPI group linked to the C-term of the protein How do ion movements during an action potential affect membrane potential? - -Influx of Na+ causes depolarization (more positive membrane potential) which triggers opening of K+ channels to restore the resting potential (more negative) Exocytosis - -Vesicles fuse with the plasma membrane, allowing substances to cross the membrane without using transporters Lipid hormones - -Move inside the cell to activate intracellular receptors What alternatives to common NSAIDs such as aspirin exist and why? - -Traditional NSAIDs target cyclooxygenases to prevent prostaglandin production and inhibit both COX-1 and COX-2; COX-2 inhibition reduces pain and inflammation but COX-1 BCHM 4611 BCHM 4611 inhibition increases the risk of stomach ulcers; COX-2 specific inhibitors are designed to inhibit only COX-2 and not COX-1 due to a steric clash Globular actin - -Actin monomer; globular shape with a cleft where ATP binds Filamentous actin - -Microfilaments formed by polymerization of globular actin; actin polymer is actually a double chain of subunits in which each subunit contacts four neighboring subunits Actin microfilaments role - -Help determine cell shape, allow some cells to move, and are part of the contractile apparatus in muscle α-tubulin and β-tubulin - -Associate to form dimers that then further assemble into microtubules Microtubules - -Help form the cytoskeleton to maintain cell shape, form a track for intracellular transport, and are part of cilia, flagella, and mitotic spindles; about three times thicker and much more rigid than actin filaments because they are constructed as hollow tubes Myosin function - -Conventional myosin (myosin II) is a motor protein that helps contract actin filaments in muscles Myosin structure - -Consists of two large polypeptides that form two globular heads attached to a long tail by two necks; each head includes a binding site for actin and a binding site for an adenine nucleotide; in the tail region, the two polypeptides twist around each other to form a single rodlike coiled coil Kinesin function - -Molecular motor that uses ATP to transport organelles along a microtubule track toward the (+) end of the microtubule Kinesin structure - -Two large globular heads and a coiled-coil tail domain; each head has a tubulin-binding site and a nucleotide-binding site; a relatively flexible polypeptide segment (the neck) joins each head to an α helix that eventually becomes part of the coiled-coil tail Activation energy (Ea or ΔG‡) - -The energy to go from the ground state (reactants) to the transition state (the peak) Catalyst - -Increases the rate of reaction by lowering the activation energy (ΔG‡) (ΔGrxn is unchanged) Catalysts alter ____ but not ____ - -Reaction rate, equilibrium; ex: enzyme will only catalyze reverse reaction if equilibrium lies far to the left, if equilibrium supports forward and reverse reactions then both will be catalyzed BCHM 4611 BCHM 4611 Divergent evolution - -Evolution from a common ancestor Convergent evolution - -Independent evolution of similar characteristics that serve the same function What proteases are an example of divergent evolution? - -3 pancreatic enzymes, all have same tertiary structure Which protease is an example of convergent evolution? - -Subtilisin (bacterial enzyme) - no sequence similarity to chymotrypsin and no overall structural similarity, but has the same Asp-His-Ser catalytic triad and an oxyanion hole in its active site Zymogen - -Inactive precursor of an enzyme How are zymogens converted to active enzymes? - -Secreted into the small intestine and cleaved by other proteases so that they acquire a conformation where the specificity pocket and oxyanion hole are available for catalysis Why are zymogens necessary? - -To limit the activity of proteases to the intestines and prevent damage to cells in other parts of the body (such as the pancreas where they are produced, and the bloodstream where they are transported) Keratin - -Structural protein that assembles into intermediate filament bundles and is present in hair, wool, nails, claws, quills, hooves, and the outer layer of skin Keratin structure - -2 long α helices wrapped around one another to form a coiled-coil; outer helix has a repeating 7 amino acid sequence where 1st and 4th a.a. of each repeat are hydrophobic; the hydrophobic side of the helix associates with the hydrophobic surface of the other monomer How does keratin form hair? - -Disulfide bonds between dimers help strengthen keratin microfibrils; covalent crosslinks form between dimers - the more crosslinks there are the greater the structural stability What types of filaments use covalent crosslinks? - -Keratin (disulfide bonds) and collagen What types of filaments use non-covalent intermolecular bonds? - -Keratin and collagen (hydrogen bonding for both) What is the role of the specificity pocket of serine proteases? - -Only binds certain amino acids, positioning the peptide bond for cleavage by the catalytic triad BCHM 4611 BCHM 4611 Chymotrypsin specificity pocket - -Gly 216, Gly 226, and Ser 189; prefers large hydrophobic side chains (ex: Phe) Irreversible inhibitor - -Reagent that permanently associates with an enzyme, inactivating it HIV life cycle - -HIV particle enters cell then disassembles; viral RNA is then transcribed into DNA by viral enzyme reverse transcriptase; another viral enzyme, an integrase, incorporates the resulting DNA into the host genome; expression of the viral genes produces 15 different proteins, some of which must be processed by HIV protease to achieve their mature forms; new viral particles are assembled and bud off from the host cell, which dies HIV reverse transcriptase - -Transcribes viral RNA into DNA HIV integrase - -Incorporates viral DNA into the host genome HIV protease - -Processes viral gene products so that they can achieve their mature forms HIV reverse transcriptase inhibitors - -1. Nucleoside analogs such as AZT and ddC readily enter cells and are phosphorylated; resulting nucleotides bind in the reverse transcriptase active site and are linked, via their 5′ phosphate group, to the growing DNA chain 2. Non-nucleoside analogs such as nevirapine, a noncompetitive inhibitor, bind to a hydrophobic patch on the surface of reverse transcriptase near the base of the thumb domain HIV protease inhibitors - -Saquinavir and ritonavir are competitive inhibitors that mimic the transition state of the reaction How do integral membrane proteins span the hydrophobic regions of the lipid bilayer? - -The portion of the protein that penetrates the lipid bilayer must have a hydrophobic surface, since the energetic cost of burying a polar protein group (and its solvating water molecules) is too great Fluid mosaic model - -Lipids and proteins may freely move laterally, but cannot move across the layer by themselves Role of cytoskeleton in fluid mosaic model - -Restricts some proteins from moving freely by anchoring them or only letting them move within a fenced-in area Lipid rafts - -Solid regions of the membrane that are high in cholesterol and sphigolipids; raft moves as a single unit within the larger membrane BCHM 4611 BCHM 4611 Uniporter - -Moves a single substance across the membrane Facilitated diffusion - -Using a protein to bind and move a substance Antiporter - -Moves 2 different substances across the membrane in opposite directions Primary active transport - -Use of ATP to drive transport Symporter - -Moves 2 different substances across the membrane in the same direction Secondary active transport - -Transmembrane transport of one substance that is driven by the free energy of an existing gradient of a second substance Passive transport - -Thermodynamically spontaneous protein-mediated transmembrane movement of a substance from high to low concentration Endocytosis - -Inward folding and budding of